Combining both genomic analysis and highEresolution imaging on a cellEbyEcell basis typically relies on customized technology which often requires significant expertise and capital cost. Cell Microsystems, Inc. has partnered with Peter Sims, PhD of Columbia University to commercialize a novel workflow for integrated imaging and sample preparation for single cell transcriptomic analysis. Dr. Sims workflow, Single Cell Optical Phenotyping and Expression Sequencing (SCOPEESeq), will be automated on a new microfluidic instrument under development by Cell Microsystems, the AIREFLOW. The system provides detailed image analysis of single cells, in addition to fullyEautomated sample preparation of single cell transcriptomic analysis (i.e. scERNAESeq). Here, we will apply this collaboratively developed platform to investigating the intractable cancer, glioblastoma. The Phase I program will use glioblastoma neurospheres as a model system to validate the system?s capabilities for: functional dye imaging, single cell molecular analysis and linking these data modalities on a cellEbyEcell basis. During the proposed Phase II these capabilities will be further tested in patientEderived biopsies to test the tumor cell specificity of fluorescent dyes used during surgical brain tumor resection. We expect the resulting system to have significant impact in this field, as well as considerable commercial potential in the broader market.